From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 28 Jan 2015 03:20:29 +0000 (+0000)
Subject: compactor work
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6c436b1b2252d9d0fb42856a5285def7858399e4;p=jalview.git

compactor work
---

diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java
index 15c2d4c..daa6166 100644
--- a/forester/java/src/org/forester/application/msa_compactor.java
+++ b/forester/java/src/org/forester/application/msa_compactor.java
@@ -418,20 +418,20 @@ public class msa_compactor {
                                               WWW,
                                               ForesterUtil.getForesterLibraryInformation() );
         System.out.println( "Input MSA                            : " + in );
-        System.out.println( "  MSA length                         : " + msa.getLength() );
-        System.out.println( "  Number of sequences                : " + msa.getNumberOfSequences() );
-        System.out.println( "  Median sequence length             : " + NF_1.format( initial_msa_stats.median() ) );
-        System.out.println( "  Mean sequence length               : "
+        System.out.println( "MSA length                         : " + msa.getLength() );
+        System.out.println( "Number of sequences                : " + msa.getNumberOfSequences() );
+        System.out.println( "Median sequence length             : " + NF_1.format( initial_msa_stats.median() ) );
+        System.out.println( "Mean sequence length               : "
                 + NF_1.format( initial_msa_stats.arithmeticMean() ) );
-        System.out.println( "  Max sequence length                : " + ( ( int ) initial_msa_stats.getMax() ) );
-        System.out.println( "  Min sequence length                : " + ( ( int ) initial_msa_stats.getMin() ) );
-        System.out.println( "  Gap ratio                          : "
+        System.out.println( "Max sequence length                : " + ( ( int ) initial_msa_stats.getMax() ) );
+        System.out.println( "Min sequence length                : " + ( ( int ) initial_msa_stats.getMin() ) );
+        System.out.println( "Gap ratio                          : "
                 + NF_4.format( MsaMethods.calcGapRatio( msa ) ) );
-        System.out.println( "  Mean gap count per 100 residues    : "
+        System.out.println( "Mean gap count per 100 residues    : "
                 + NF_1.format( MsaMethods.calcNumberOfGapsPer100Stats( msa ).arithmeticMean() ) );
-        System.out.println( "  Normalized Shannon Entropy (entn7) : "
+        System.out.println( "Normalized Shannon Entropy (entn7) : "
                 + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 7, msa ) ) );
-        System.out.println( "  Normalized Shannon Entropy (entn21): "
+        System.out.println( "Normalized Shannon Entropy (entn21): "
                 + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 21, msa ) ) );
     }